what are three major themes you would identify that connect the various topics discussed in the course

This semester we have discussed basic chemical principles and looked at the nature of different molecules that make up all living creatures. Metabolism brought all of this together and showed how the bulk of chemical reactions of biomolecules function within us all and is the basis for life itself. But in order for metabolism to occur structures need to be formed so that open systems can be achieved and biomolecules can be used efficiently. This is why DNA replication and protein synthesis are two other important process we have learned and all three of these connect with all the topics we have discussed.
DNA replication forms a template strand that is transcribed into RNA and is then translated into specific proteins and it is involved and influences all other processes within an organism. It designs the proteins needed for metabolism, the enzymes used to catalyze metabolic reactions and designs the systems needed for these reactions occur.
Proteins are like the, “local handy man” and seem to be able to do any task given to them. They are involved in every process even the synthesis of themselves. Proteins work in the building and repairing of body tissues, regulates body processes and formation of enzymes and hormones. Our body needs proteins for the purpose of maintenance and healthy growth.
Metabolism, DNA replication and the synthesis of proteins are topics that seem to come up over and over again in all my classes; Biochemistry has only taken them and really gone into depth as to how they work. Now I know that transcription and translation factors are extremely important in synthesis of new proteins. Apparently I only knew the basics behind synthesis (which was fine with me), DNA replicates by DNA polymerase binding, A-T, C-G and U is involved in RNA translation and synthesis of proteins. Now I know it is extremely complicated and that there important protein factors that must bind too DNA first before Polymerase is even in the picture.
In biochemistry it seems every class I am learning about a new protein and how important it is. Transcription and translation factors of pre-initiation complexes, to Enzymes and co-enzymes in catalyzing reactions of metabolic pathways each week there is a new protein to understand.
Metabolism has been the same case. I knew the basics glycolysis and the metabolic pathway of glucose to form ATP NAD and FAD. Now I know what reaction occurs in steps of glycolysis and the enzymes used for these different reactions if they are exorgonic or endorgonic reactions. We also went into greater detail as to how lactate is synthesized back into glucose which I found very interesting because I didn’t know that these reactions in glycolysis for the most part can go both ways.

How would you explain the connection between glucose and the energy created by the body to a friend.

One of my friends asks me to explain, “How glucose works in the body”. This is a scenario that is very unlikely. If this were to happen though I would explain to them that glucose is a major source of energy that the cells in your body use to function properly. Glucose comes from carbohydrates which are found the foods we eat like vegetables, fruits, grains. Glucose is one the main products of photosynthesis in plants. When you eat a piece of bread your body takes those carbohydrates and breaks them down into simple sugars of glucose. This occurs in your mouth, stomach and small intestine where carbohydrates, a polysaccharide (basically a big bundle of sugars) are broken down into monosaccharides, which are mainly glucose molecules.
Once broken down the body absorbs these glucose molecules into the blood where they travel around the body and used for energy. Glucose is stored in the body by synthesis of glycogen, which can be found in muscle tissue and the liver. Glycogen is like a vine of grapes where is grape is a glucose molecule. When levels of glucose are low in the blood your pancreas excretes insulin which will increase blood glucose levels by the breakdown of glycogen.
Now glucose is used as energy by a process called glycolysis which is the breakdown of glucose. This process takes glucose and breaks it down into 2 pyruvate acid molecules. During this process 2 ATP molecules where formed. ATP is the energy that is used in all in the body, think of it as the body’s own currency that all processes can use for energy in order to function. Glycolysis forms 4 ATP but in order for that to occur it to occur it takes 2 ATP for glycolysis to function. Your body can use this pyruvate to form lactate when oxygen is not available, which will then be transported by the blood to the liver where it can be synthesized back into glucose. If oxygen is available then it can further be turned into more ATP by 2 other metabolic processes.
Glycolysis forms 2 ATP, for every one glucose molecule. That is really not a lot of energy, so pyruvate can further make ATP by turning Pyruvate into Acetyl CoA which is used in Kreb’s cycle. This cycle forms two different molecules NAD and FAD which will be used in another process. These are coenzymes that are used to take the proton H+ and change a chemical gradient within a process called electron transport chain. Here is where more ATP is formed. The H+ chemical gradient creates an electrical gradient that promotes the formation of at least 30 ATP per for every glucose molecule.

What knowledge of you connected with past knowledge

In my physiology class we talked a lot about how metabolism works in the body and how important it is to have a balanced diet so that metabolic process can work properly. It provides the needed energy and nutrition to maintain cells, tissues, organs, and sustain optimal growth and development. Having a well-balanced diet involves eating foods in healthy proportions from all food groups. Fats, carbohydrates, protein, vitamins, fiber, and mineral salts, each of these nutrients are vital pieces in the function of the human body. A balanced diet helps maintain a good supply of nutrients which in turn keeps the body metabolism working properly.
Taking this knowledge and applying it in biochemistry has been very beneficial in understanding metabolic processes. We touched base on the steps of glycolysis, TCA cycle and the electron chain transport in Physiology but not as in depth as we did in biochemistry. Understanding how different enzymes catalyze different reactions within each step has helped in understanding the big picture.
Biochemistry has also helped further my knowledge of hormones, steroids and other molecules are used in the body. I already knew what they did but what I didn’t know is how they are formed. Now I know at a molecular level how they are formed thanks to biochemistry.

Find a protein using PDB explorer-describe your protein, include what disease state or real-world application it has

Deoxyhemoglobin A



Deoxyhemoglobin S

Hemoglobin is a protein located within red blood cells. Its function is to transport oxygen from the lungs to the rest of the body. It also retrieves carbon dioxide transporting it back to the lungs. Normal hemoglobin structure contains both a tertiary and quaternary structures of a protein. The majority of the amino acids form alpha helices which are stabilized by hydrogen bonds. Its quaternary structure is formed by four globular protein subunits in a tetrahedral arrangement. Normal hemoglobin subunits contain 2 alpha chains and 2 beta chains which are arranged into Alpha-helix structured segments that bind to the non-protein Heme groups. Within the Heme group contains an iron charged ion which is the binding site of oxygen molecules.

Above the left picture is an example of “deoxyhemoglobin A” (“Deoxy”, when iron is not bound to any oxygen molecule). This is the typical shape of a normal hemoglobin molecule. The right picture is an example of deoxyhemoglobin S. This is a mutated hemoglobin molecule which is the cause for sickle cell disease. Sickle cell disease is a blood disorder brought on by abnormal hemoglobin forming a sickle shaped red blood cell.

Comparing these two photos helps you understand why the structure of proteins is so important to their function.

Sickle cell disease is a genetic disorder brought on by the mutation of the beta globin chain causing the hydrophilic amino acid glutamic to be replacing with a hydrophobic amino acid valine. When there are two abnormal Beta globin subunits bound to 2 alpha globin subunits, it will form Hemoglobin S.

http://en.wikipedia.org/wiki/Sickle_cell_disease

http://en.wikipedia.org/wiki/Hemoglobin

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1118

What knowledge have you connected with past knowledge?

I graduated last year from Plymouth State University with a Bachelors of Science in Business Management. Then I realized that I wanted to become a Physician Assistant. So here I am now at UNH Manchester, trying to fulfill my science prerequisites for the PA program. People said I was crazy being a full time student and taking only science classes, as did I at first. But over the fall semester I realized that this was a great way to take in the plethora of information within these courses because they all coincide with one another.

Last semester I took Biology, Chemistry, and Anatomy and the concepts I learned from each class seem to build on top of each other. Now I am taking Chemistry, Biochemistry, and Anatomy. The concepts we have learned in Biochemistry have touched base with all material I have learned in other science courses.

In biology we learned about structure of organic molecules like proteins. I got to understand the basis behind a protein and how they are made. I knew only the basics behind a protein and now biochemistry has really helped me understand the process behind primary, secondary, tertiary, quaternary structures of a protein and its subunits. Biochemistry has also been a big help in Anatomy. My last test in Anatomy was on the endocrine system. It was discussing the physiological aspects of steroids in my anatomy and then I would go more in depth into the structure and function of steroids in biochemistry. Biochemistry has also allowed me to use formulas and laws that I have learned in chemistry.

That is what I like about science; all fields are connected in some way. I get to take concepts from one course and then apply them to other fields in science. Biochemistry has touched base on everything I have learned in the past year, but took it one step further.

Find an interesting biochemistry website and put its link in the entry, and describe briefly what is found here.

http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm

I am a visual learner and by combining the complex processes that I learn in lecture and from my text with animations really helps me grasp the whole picture. Wiley.com has been a fun way for me to understand complex biochemical concepts.

When we started learning about amino acids I had problems remembering the structure of the 20 different amino acids. http://www.wiley.com/legacy/college/boyer/0470003790/animations/acideroids/acideroids.htm This game is called, “Acideroids”. It is kind of like the old Nintendo game “Asteroids”, except now the asteroids are different amino acids. You are in control of a ship that must pass through a field of acideroids and the only way to get through is to shoot and destroy the correct amino acid. I played for about an hour one day and by the end of my mission I knew structure of all 20 amino acids.

The "Cutting Edge", window within this website I found really interesting. It features articles on exciting developments within the field of biochemistry. I read an interesting article on Telomeres and how it could be the Holy Grail for eternal life and possible treatment for cancer patients.

This site has animations and tutorials that take you through critical structural and functional features of biomolecules. Every concept we have talked about in class you will find something about it here. Tests are also available take after each tutorial. It is a hands on way to grasp the big picture behind all concepts in Biochemistry. Check it out!

What is biochemistry, and how does it differ from the fields of genetics, biology, chemistry, and molecular biology

Biochemistry is the study of life in its chemical processes. This discipline emerged at the beginning of the 20^th century. Scientists began to combined chemistry, physiology and biology to investigate the chemistry of living organisms. It is seen as a life science and chemical science because it explores the chemistry within living organism.

Biochemistry is branched off from biology, chemistry, and now genetics. When comparing biology and biochemistry, picture them as micro and macro levels of life science.

At the Macro level Biology is the study of life and living organism, researching from the molecular and larger. Biologist's will look at these molecules and see how they interact with one another but focus on how they perform cellular tasks within an organism. They focus on their structure, function, growth, origin, and how they evolved in their biological system.

At the micro level, Biochemist's looks at how electrons, atoms, and molecules behave in biological systems, researching at the molecular level and smaller. Focusing on , structure, function, origin, and formation of molecules at the micro level.

Chemistry is the scientific study of matter, its properties, and interactions with other matter and energy. Biochemistry was branched off from chemistry because it looks at organic molecules of the periodic table and they relate and interact within biological systems.

Genetics is the study common traits within organism from previous generations. Common traits are described by genetic information carried by the molecule DNA. This is where the blueprints for constructing and operating an organism are contained. All living things contain DNA and biochemistry uses this knowledge to understand how molecules are formed within organisms. Biochemist’s want to learn the structure and function of cellular components like proteins, carbohydrates, lipids, nucleic acids, and other molecules within a biological system.

http://chemistry.about.com/od/chemistry101/a/basics.htm

http://www.medhelp.org/medical-information/show/1217/Genetics